7:30a – 11:15a
General stuff
- installed windows updates on Monet
- installed new RAM (now 32GB)
- sent (final?) version of Banff report to co-organizers. Send to BIRS on Mon.
Chromatin simulations
- functionalizing chromatin simulation code
- attempting to increase simulation speed
- distance calculations between nodes were a major slowdown. These have been sped up with sqdistance. I don’t see how pdist works. I want a matrix of all pairwise distances of 3D vectors, and neither orientation of passing it input seems to give what I want.
- intuitive implementation of pdist = `Z = squareform(pdist(D))’
- but it’s probably faster still to work with the assymetric case, (i.e. let’s use it without squareform);
- pdist is definetely faster than sqdistance.
- Substantially accelerated code.
- See if we can get sizable simulations still to be able to complete in less than 24 hours. Then we can run hundreds in parallel on Odyssey and get population statistics and contact maps.
- Running logscale increment from 10 to 1024 free polymer simulations to compute scaling
- Preliminary linear exploration:
Project 2
- Troubleshooting warp with mRNA alignment
- basically working now.
- explain details to Hao on Monday
- drive arrived, set-up project on Cajal or Tuck on Monday.
- see notes.
STORM Analysis
- Modifying chromatin cropper
- make drift correction its own step
Cell Culture
- check cells — mostly still attached (that’s good at least), seem to be growing slowly.